UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures

Lua, Rhonald C.; Wilson, Stephen J.; Konecki, Daniel M.; Wilkins, Angela D.; Venner, Eric; Morgan, Daniel H.; Lichtarge, Olivier

doi:10.1093/nar/gkv1279

Cited by 33 publications

(31 citation statements)

References 37 publications

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“…In order to compute the probability that the residue combinations constituting disordered patches or N-linked glycosylation neighborhoods likely represent clusters of function-determining residues, full length protein sequences were input into the Universal Evolutionary Trace server (http://lichtargelab.org/software/uet) 34 . The evolutionary trace of residues that varies among evolutionarily distant protein homologs is ranked higher than for residues that vary among evolutionarily proximal protein homologs 35 . The program searches for all homologous sequences within the Uniref90 database (with a minimum e-value cutoff of 1e-250) up to 500 sequences.The mean of residue ranks was computed and compared between Statistics.…”

Section: Methodsmentioning

confidence: 92%

Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins

Goutham¹,

Kumari

Pally³

et al. 2020

Sci Rep

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Several post-translational protein modifications lie predominantly within regions of disorder: the biased localization has been proposed to expand the binding versatility of disordered regions. However, investigating a representative dataset of 500 human N-glycoproteins, we observed the sites of n-linked glycosylations or n-glycosites, to be predominantly present in the regions of predicted order. When compared with disordered stretches, ordered regions were not found to be enriched for asparagines, serines and threonines, residues that constitute the sequon signature for conjugation of N-glycans. We then investigated the basis of mutual exclusivity between disorder and N-glycosites on the basis of amino acid distribution: when compared with control ordered residue stretches without any N-glycosites, residue neighborhoods surrounding N-glycosites showed a depletion of bulky, hydrophobic and disorder-promoting amino acids and an enrichment for flexible and accessible residues that are frequently found in coiled structures. When compared with control disordered residue stretches without any N-glycosites, N-glycosite neighborhoods were depleted of charged, polar, hydrophobic and flexible residues and enriched for aromatic, accessible and order-promoting residues with a tendency to be part of coiled and β structures. N-glycosite neighborhoods also showed greater phylogenetic conservation among amniotes, compared with control ordered regions, which in turn were more conserved than disordered control regions. our results lead us to propose that unique primary structural compositions and differential propensities for evolvability allowed for the mutual spatial exclusion of n-glycosite neighborhoods and disordered stretches.One of the common co-and post-translational modifications of polypeptides is the conjugation of branched glycosylations to asparagines (known as N-linked glycosylations) 1 . N-linked glycosylation begins with the assembly of an oligosaccharide on dolichol pyrophosphate and the subsequent transfer of the oligosaccharide to the asparagine residues of polypeptides in the lumen of the endoplasmic reticulum; the oligosaccharide is further remodeled in the Golgi complex. Several proteins that end up in the extracellular milieu or as transmembrane proteins are N-linked glycoconjugates. The establishment of organismal morphologies has been sought to be understood through the interactions of a highly conserved set of proteins known as the developmental genetic toolkit 2 . Most toolkit proteins, which are involved in tissue-scale processes, such as cell-cell and cell-matrix adhesion, diffusion-driven signaling and cell movement, are extracellular-or membrane-bound glycoproteins 3,4 . The fundamental role of such toolkit proteins in mechanisms of organ-and organismal-development across diverse clades suggests evolutionary constraints on their structures and folds, while they may have continued to evolve to perform newer functions as organisms occupied and constructed newer niches.A large number of eukaryotic pro...

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Section: Methodsmentioning

confidence: 92%

Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins

Goutham¹,

Kumari

Pally³

et al. 2020

Sci Rep

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“…Using the Universal Evolutionary Trace method [36], residues of TmrA and TmrB were assigned a coverage score correlating with functional importance and in which residues with a lower score (higher inverse score) are considered more functionally important. As expected, residues in multiple known motifs in the NBDs ranked in the top 5% (above 95% rank) (Figure 2A).…”

Section: Evolutionary Contact Predictions Show the Psm Connects Nbds mentioning

confidence: 99%

“…Analysis of evolutionarily conserved networks is a powerful approach for inferring conserved mechanisms of allostery from sequence. Here, two complimentary evolutionary analysis methods were used to identify such networks in the understudied, but critical, TmrAB exporter ICL region: Evolutionary Trace [35] to identify conserved single residues important for function and Evolutionary Couplings [36,37] to identify conserved contacts between pairs of residues.…”

Section: Mutation Of the 100% Conserved Psm Glycines Block The Abilitmentioning

confidence: 99%

The peptide sensor motif stabilizes the outward-facing conformation of TmrAB

Millan

Francis

Thompson

et al. 2020

Preprint

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ATP binding cassette (ABC) transporters participate in many processes central to life including cell wall biosynthesis, lipid homeostasis, and drug efflux. Large conformational rearrangements accompany transport and allosterically couple substrate transport in the transmembrane region to dimerization of nucleotide binding domains (NBDs) nearly ~30-40Å away in the cytoplasm. How the two binding sites coordinate remains elusive, particularly in a class of ABC transporters with only one catalytically competent NBD, the asymmetric ABC transporters. The peptide transporter TmrAB from Thermus thermophilus is one such asymmetric transporter, and here we present biochemical evidence that substrate binding couples to ATP binding in nonequivalent ways through each half of the TmrAB heterodimer. Specifically, we show that this unique mechanism depends on a highly conserved electrostatic motif in a region previously termed the peptide sensor. In this conformationally dynamic region, we demonstrate that mutation of an absolutely conserved glycine in the catalytically active TmrA chain (G131A) accelerates ATPase activity while uncoupling substrate binding from ATP hydrolysis. Surprisingly, mutation of the conserved glycine in the non-functional TmrB chain (G116A) resulted in the opposite effect in which ATPase activity is decreased with little effect on substrate binding. Our findings highlight an intrinsic asymmetry extending beyond that of the NBDs in asymmetric ABC transporters and support a mechanism where the peptide sensor in each half of TmrAB plays different roles in substrate transport.

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“…Protein sequences are the fundamental determinants of biological structure and function. [37] The field of structural biology has provided a plethora of knowledge on protein structure enabling prediction for the translation of a protein's primary sequence, through secondary structure (such as alpha helices, beta sheets, turns etc) to common motifs, domains, folds, tertiary and even quaternary arrangement of subunits. [38] Homology modelling is a technique which builds a 3D structure from a protein sequence of interest based on the 3D structure of a similar protein.…”

Section: Homology Modellingmentioning

confidence: 99%

A Practical Guide to Molecular Docking and Homology Modelling for Medicinal Chemists

Lohning

Levonis

Williams-Noonan

et al. 2017

CTMC

130

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Elucidating details of the relationship between molecular structure and a particular biological end point is essential for successful, rational drug discovery. Molecular docking is a widely accepted tool for lead identification however, navigating the intricacies of the software can be daunting. Our objective was therefore to provide a step-by-step guide for those interested in incorporating contemporary basic molecular docking and homology modelling into their design strategy. Three molecular docking programs, AutoDock4, SwissDock and Surflex-Dock, were compared in the context of a case study where a set of steroidal and non-steroidal ligands were docked into the human androgen receptor (hAR) using both rigid and flexible target atoms. Metrics for comparison included how well each program predicted the X-ray structure orientation via root mean square deviation (rmsd), predicting known actives via ligand ranking and comparison to biological data where available. Benchmarking metrics were discussed in terms of identifying accurate and reliable results. For cases where no three dimensional structure exists, we provided a practical example for creating a homology model using Swiss-Model. Results showed an rmsd between X-ray ligands from wild-type and mutant receptors and docked poses were 4.15Å and 0.83Å (SwissDock), 2.69Å and 8.80Å (AutoDock4) and 0.39Å and 0.71Å (Surflex-Dock) respectively. Surflex-Dock performed consistently well in pose prediction (less than 2Å) while Auto- Dock4 predicted known active non-steroidal antiandrogens most accurately. Introducing flexibility into target atoms produced the largest degree of change in ligand ranking in Surflex-Dock. We produced a viable homology model of the P2X1 purireceptor for subsequent docking analysis.

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UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures

Cited by 33 publications

References 37 publications

Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins

Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins

The peptide sensor motif stabilizes the outward-facing conformation of TmrAB

A Practical Guide to Molecular Docking and Homology Modelling for Medicinal Chemists

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